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In this paper, a two-patch model with additive Allee effect, nonlinear dispersal and commensalism is proposed and studied. The stability of equilibria and the existence of saddle-node bifurcation, transcritical bifurcation are discussed. Through qualitative analysis of the model, we know that the persistence and the extinction of population are influenced by the Allee effect, dispersal and commensalism. Combining with numerical simulation, the study shows that the total population density will increase when the Allee effect constant a increases or m decreases. In addition to suppress the Allee effect, nonlinear dispersal and commensalism are crucial to the survival of the species in the two patches. [ABSTRACT FROM AUTHOR]

Twitter and Facebook are widely recognized as crucial tools for situational information during disasters. Given that the classification of disaster related tweets is computationally challenging due to the high dimension of textual data caused by the redundant and irrelevant features. Hence for optimal feature selection (FS) and classification of disaster tweets, this work utilizes binary salp swarm algorithm (BSSA) and proposed two enhancements over it (PBcSSA). The commensalism phase from symbiotic organisms search (SOS) is integrated with BSSA to enhance its feature space searchability and then its parallel implementation is done using Apache Spark framework to reduce the execution time. The experiments were performed in a cross-disaster setting on nine groups of datasets including biological, earthquake, flood, hurricane, industrial, societal, transportation, wildfire, and environmental. The proposed PBcSSA combined with the Naive Bayes (NB) classifier in wrapper mode and its performance is compared with standard BSSA, binary sine cosine algorithm (BSCA), binary particle swarm optimization (BPSO), binary grey wolf optimization (BGWO), and binary whale optimization algorithm (BWOA). The experimental results reveal that the proposed PBcSSA outperforms other algorithms in disaster tweet classification and achieved highest average F1-score with lowest feature set in a reduced execution time. [ABSTRACT FROM AUTHOR]

The paper explores the dynamic relationship between sharksuckers and Atlantic Nurse sharks within a fish cleaning station in South Eleuthera, The Bahamas. Despite the prevalent symbiotic association between echeneid fishes and sharks, the specifics of their interactions, behavioral adaptations, and the influence of food availability remain understudied. The research employed a comprehensive observational approach, focusing on free-swimming and attached sharksucker' behaviors (Echeneis spp.) in the presence of Atlantic Nurse sharks. Through a month-long study, both qualitative and quantitative analyses of the behaviors were conducted. The results challenge the traditional perception of a purely mutualistic or parasitic relationship, suggesting a more complex dynamic between sharksuckers and sharks. Specifically, the study indicates an increase in boldness and competitive behaviors towards sharks in a controlled feeding setting, indicating that sharksuckers' behaviors and relationships with their hosts are constantly evolving and should not be treated as simply symbiotic. [ABSTRACT FROM AUTHOR]

The commensal symbiosis system with the Allee effect and single feedback control is proposed and analyzed in this paper. The stability analysis of all possible equilibrium points is discussed, and the sufficient conditions for global stability of the interior equilibrium points are obtained. The occurrence of transcritical bifurcation and saddle-node bifurcation around the equilibrium points is investigated. Finally, the main results of the model are illustrated by numerical simulations. [ABSTRACT FROM AUTHOR]

Symbionts dominate planetary diversity and three primary symbiont diversification processes have been proposed: co-speciation with hosts, speciation by host-switching, and within-host speciation. The last mechanism is prevalent among members of an extraordinary marine symbiosis in the Indian River Lagoon, Florida, composed of a host mantis shrimp, Lysiosquilla scabricauda, and seven host-specific commensal vasconielline "yoyo" clams (Galeommatoidea) that collectively occupy two distinct niches: burrow-wall-attached, and host-attached/ectocommensal. This within-host symbiont radiation provides a natural experiment to test how symbiont coexistence patterns are regulated in a common ancestral habitat. The competitive exclusion principle predicts that sister taxa produced by adaptive speciation (with distinct morphologies and within-burrow niches) are most likely to coexist whereas the neutral theory predicts no difference among adaptive and non-adaptive sister taxa co-occurrence. To test these predictions, we engaged in (1) field-censusing commensal species assemblages; (2) trophic niche analyses; (3) laboratory behavioral observations. Although predicted by both models, the field census found no mixed-niche commensal assemblages: multi-species burrows were exclusively composed of burrow-wall commensals. Their co-occurrence matched random assembly process expectations, but presence of the single ectocommensal species had a highly significant negative effect on recruitment of all burrow-wall commensal species (P < 0.001), including on its burrow-wall commensal sister species (P < 0.001). Our stable isotope data indicated that commensals are suspension feeders and that co-occurring burrow-wall commensals may exhibit trophic niche differentiation. The artificial burrow behavioral experiment yielded no evidence of spatial segregation among burrow-wall commensals, and it was terminated by a sudden breakdown of the host-commensal relationship resulting in a mass mortality of all commensals unattached to the host. This study system appears to contain two distinct, superimposed patterns of commensal distribution: (1) all burrow-wall commensal species; (2) the ectocommensal species. Burrow-wall commensals (the plesiomorphic condition) broadly adhere to neutral theory expectations of species assembly but the adaptive evolution of ectocommensalism has apparently led to ecological exclusion rather than coexistence, an inverse outcome of theoretical expectations. The ecological factors regulating the observed burrow-wall/ectocommensal exclusion are currently obscure but potentially include differential recruitment to host burrows and/or differential survival in "mixed" burrow assemblages, the latter potentially due to changes in host predatory behavior. Resampling host burrows during commensal recruitment peak periods and tracking burrow-wall commensal survival in host burrows with and without added ectocommensals could resolve this outstanding issue. [ABSTRACT FROM AUTHOR]

Background: The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess clinically significant antibiotic resistance genes. Among these opportunistic pathogens, the Klebsiella genus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, the essential transmission factors influencing the spread of Klebsiella species among both healthy and diseased individuals remain unclear. Results: Here, we explored a possible explanation by investigating the ability of oral and nasal Klebsiella species to outcompete their native microbial community members under in vitro starvation conditions, which could be analogous to external hospital environments or the microenvironment of mechanical ventilators. When K. pneumoniae and K. aerogenes were present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became enriched in Klebsiella species. Furthermore, introducing K. pneumoniae exogenously into a native microbial community lacking K. pneumoniae, even at low inoculum, led to repeated enrichment under starvation. Precise monitoring of K. pneumoniae within these communities undergoing starvation indicated rapid initial growth and prolonged viability compared to other members of the microbiome. K. pneumoniae strains isolated from healthy individuals' oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence of Klebsiella species, other understudied opportunistic pathogens, such as Peptostreptococcus, increased in relative abundance under starvation conditions. Conclusions: Our findings establish an environmental and microbiome community circumstance that allows for the enrichment of Klebsiella species and other opportunistic pathogens. Klebsiella's enrichment may hinge on its ability to quickly outgrow other members of the microbiome. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions could be an important factor that contributes to enhanced transmission in both commensal and pathogenic contexts. 2NMbQE6jVjinwr48dC_rNo Video Abstract [ABSTRACT FROM AUTHOR]

Interactions between bacterial microbiota and epibenthic species of the dinoflagellate Prorocentrum may define the onset and persistence of benthic harmful algal blooms (bHABs). Chemical ecological interactions within the dinoflagellate phycosphere potentially involve a complex variety of organic molecules, metabolites, and toxins, including undefined bioactive compounds. In this study, the bacterial diversity and core members of the dinoflagellate-associated microbiota were defined from 11 strains of three epibenthic Prorocentrum species, representing three geographically disjunct locations within Mexican coastal waters. Microbiota profiles in stable monoclonal Prorocentrum cultures were obtained by sequencing amplicons of the V3-V4 region of the 16S rRNA gene. Thirteen classes of bacteria were identified among dinoflagellate clones, where Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia were consistently dominant. The bacterial community structure exhibited significantly different grouping by the location of origin of dinoflagellate clones. No significant diversity difference was found among free-living or unattached bacteria in the dinoflagellate culture medium (M) compared with those in closer association with the dinoflagellate host cells (H). Twelve taxa were defined as core members of the bacterial assemblage, representing the genera Algiphilus, Cohaesibacter, Labrenzia, Mameliella, Marinobacter, Marivita, Massilia, Muricauda, Roseitalea, and an unclassified member of the Rhodobacteraceae. The core members are inferred to significantly contribute to primary and secondary metabolic functions, but no direct correlation with dinoflagellate toxigenicity was apparent. Overall the bacterial profile and implied gene functionality indicated a suite of positive interactions, suggesting either mutualism or commensalism with the dinoflagellate. The further characterization and interpretation of specific gene functions and interactions between bacteria and dinoflagellates, such as epibenthic members of genus Prorocentrum, are key to understanding their role in toxigenesis and bHAB development. [ABSTRACT FROM AUTHOR]

Co-aggregation of anaerobic microorganisms into suspended microbial biofilms (aggregates) serves ecological and biotechnological functions. Tightly packed aggregates of metabolically interdependent bacteria and archaea play key roles in cycling of carbon and nitrogen. Additionally, in biotechnological applications, such as wastewater treatment, microbial aggregates provide a complete metabolic network to convert complex organic material. Currently, experimental data explaining the mechanisms behind microbial co-aggregation in anoxic environments is scarce and scattered across the literature. To what extent does this process resemble co-aggregation in aerobic environments? Does the limited availability of terminal electron acceptors drive mutualistic microbial relationships, contrary to the commensal relationships observed in oxygen-rich environments? And do co-aggregating bacteria and archaea, which depend on each other to harvest the bare minimum Gibbs energy from energy-poor substrates, use similar cellular mechanisms as those used by pathogenic bacteria that form biofilms? Here, we provide an overview of the current understanding of why and how mixed anaerobic microbial communities co-aggregate and discuss potential future scientific advancements that could improve the study of anaerobic suspended aggregates. Key points: • Metabolic dependency promotes aggregation of anaerobic bacteria and archaea • Flagella, pili, and adhesins play a role in the formation of anaerobic aggregates • Cyclic di-GMP/AMP signaling may trigger the polysaccharides production in anaerobes [ABSTRACT FROM AUTHOR]

Remoras are a highly specialised group of fishes known to associate with a range of marine megafauna, including elasmobranchs, cetaceans and marine reptiles. Remoras appear to benefit from these interspecific interactions through consumption of host dermal parasites or reduced cost of transport. Shark‐remora associations are widely documented, yet our understanding of the costs and benefits involved in these interactions is poor. Studies frequently make claims about mutualistic, commensalistic or parasitic relationships without providing the necessary quantitative information necessary to make these claims. Here I explain why this approach is problematic, and proceed to examine shark‐remora interactions in a rigorous eco‐evolutionary framework. These interactions cannot be properly classified without considering net evolutionary fitness and context dependence. In reality, shark‐remora interactions are best defined by a multidimensional spectrum of fitness consequences, with net fitness outcomes shifting between mutualism and parasitism (and vice versa) through space and time. [ABSTRACT FROM AUTHOR]

Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system and a leading cause of neurological disability in young adults. Clinical presentation and disease course are highly heterogeneous. Typically, disease progression occurs over time and is characterized by the gradual accumulation of disability. The risk of developing MS is driven by complex interactions between genetic and environmental factors, including the gut microbiome. How the commensal gut microbiota impacts disease severity and progression over time remains unknown. In a longitudinal study, disability status and associated clinical features in 58 MS patients were tracked over 4.2 ± 0.98 years, and the baseline fecal gut microbiome was characterized via 16S amplicon sequencing. Progressor status, defined as patients with an increase in Expanded Disability Status Scale (EDSS), were correlated with features of the gut microbiome to determine candidate microbiota associated with risk of MS disease progression. We found no overt differences in microbial community diversity and overall structure between MS patients exhibiting disease progression and non-progressors. However, a total of 41 bacterial species were associated with worsening disease, including a marked depletion in Akkermansia, Lachnospiraceae, and Oscillospiraceae, with an expansion of Alloprevotella, Prevotella-9, and Rhodospirillales. Analysis of the metabolic potential of the inferred metagenome from taxa associated with progression revealed enrichment in oxidative stress-inducing aerobic respiration at the expense of microbial vitamin K2 production (linked to Akkermansia), and a depletion in SCFA metabolism (linked to Oscillospiraceae). Further, as a proof of principle, statistical modeling demonstrated that microbiota composition and clinical features were sufficient to predict disease progression. Additionally, we found that constipation, a frequent gastrointestinal comorbidity among MS patients, exhibited a divergent microbial signature compared with progressor status. These results demonstrate a proof of principle for the utility of the gut microbiome for predicting disease progression in MS in a small well-defined cohort. Further, analysis of the inferred metagenome suggested that oxidative stress, vitamin K2, and SCFAs are associated with progression, warranting future functional validation and mechanistic study. [ABSTRACT FROM AUTHOR]

Background: Staphylococcus aureus, a commensal bacterium, colonizes the skin and mucous membranes of approximately 30% of the human population. Apart from conventional resistance mechanisms, one of the pathogenic features of S. aureus is its ability to survive in a biofilm state on both biotic and abiotic surfaces. Due to this characteristic, S. aureus is a major cause of human infections, with Methicillin-Resistant Staphylococcus aureus (MRSA) being a significant contributor to both community-acquired and hospital-acquired infections. Results: Analyzing non-repetitive clinical isolates of MRSA collected from seven provinces and cities in China between 2014 and 2020, it was observed that 53.2% of the MRSA isolates exhibited varying degrees of ability to produce biofilm. The biofilm positivity rate was notably high in MRSA isolates from Guangdong, Jiangxi, and Hubei. The predominant MRSA strains collected in this study were of sequence types ST59, ST5, and ST239, with the biofilm-producing capability mainly distributed among moderate and weak biofilm producers within these ST types. Notably, certain sequence types, such as ST88, exhibited a high prevalence of strong biofilm-producing strains. The study found that SCCmec IV was the predominant type among biofilm-positive MRSA, followed by SCCmec II. Comparing strains with weak and strong biofilm production capabilities, the positive rates of the sdrD and sdrE were higher in strong biofilm producers. The genetic determinants ebp, icaA, icaB, icaC, icaD, icaR, and sdrE were associated with strong biofilm production in MRSA. Additionally, biofilm-negative MRSA isolates showed higher sensitivity rates to cefalotin (94.8%), daptomycin (94.5%), mupirocin (86.5%), teicoplanin (94.5%), fusidic acid (81.0%), and dalbavancin (94.5%) compared to biofilm-positive MRSA isolates. The biofilm positivity rate was consistently above 50% in all collected specimen types. Conclusions: MRSA strains with biofilm production capability warrant increased vigilance. [ABSTRACT FROM AUTHOR]

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The aim of this paper is to show that Tilman’s graphical method for the study of competition between two species for two resources can be advantageously used for the study of commensalism or syntrophy models, where a first species produces the substrate necessary for the growth of the second species. The growth functions of the species considered are general and include both inhibition by the other substrate and inhibition by the species’ limiting substrate, when it is at a high concentration. Because of their importance in microbial ecology, models of commensalism and syntrophy, with or without self-inhibition, have been the subject of numerous studies in the literature. We obtain a unified presentation of a large number of these results from the literature. The mathematical model considered is a differential system in four dimensions. We give a new result of local stability of the positive equilibrium, which has only been obtained in the literature in the case where the removal rates of the species are identical to the dilution rate and the study of stability can be reduced to that of a system in two dimensions. We describe the operating diagram of the system: this is the bifurcation diagram which gives the asymptotic behavior of the system when the operating parameters are varied, i.e., the dilution rate and the substrate inlet concentrations. [ABSTRACT FROM AUTHOR]

Digital platforms are increasingly dominating markets by bringing together two or more groups of users and facilitating the exchange of value between them. Although several significant issues concerning the dynamics of digital platforms have been addressed, much of the research effort has focused on the platform owner. On the other hand, research on complementors neither takes into account the individual level nor clearly shows what an individual complementor can do to benefit from platform participation. By studying the evolving relationship between YouTube and its ecosystem of complementors (content creators), we shed light on the strategies that complementors use to progressively avoid but still benefit from platform governance. We find that content creators are, first, in a mutual relationship with the YouTube platform, benefiting from direct monetization. Then, they shift to commensalism as the relationship evolves, allowing them to avoid YouTube's governance and take advantage of multi‐homing. Our findings illuminate the effects of platform governance, particularly how it shapes the actions of complementors. [ABSTRACT FROM AUTHOR]

Currently, exposome studies include a raft of different monitoring tools, including remote sensors, smartphones, omics analyses, distributed lag models, etc. The similarity in structure between the exposome and the microbiota plus their functions led us to pose three pertinent questions from this viewpoint, looking at the actual relationship between the exposome and the microbiota. In terms of the exposome, a bistable equilibrium between health and disease depends on constantly dealing with an ever-changing totality of exposures that together shape an individual from conception to death. Regarding scientific knowledge, the exposome is still lagging in certain areas, like the importance of microorganisms in the equation. The human microbiome is defined as an aggregate assemblage of gut commensals that are hosted by our surfaces related to the external environment. Commensals' resistance to a variety of environmental exposures, such as antibiotic administration, confirms that a layer of these organisms is protected within the host. The exposome is a conceptual framework defined as the environmental component of the science-inspired systems ideology that shifts from a specificity-based medical approach to reasoning in terms of complexity. A parallel concept in population health research and precision public health is the human flourishing index, which aims to account for the numerous environmental factors that affect individual and population well-being beyond ambient pollution. [ABSTRACT FROM AUTHOR]

The monotypic polynoid genus Arctonoella Buzhinskaja, 1967 comprises solely the type species A. sinagawaensis (Izuka, 1912), which was originally described from Tokyo Bay (central Japan), and subsequently recorded from China and the Russian Far East. The six specimens we collected together with the burrowing filter-feeding spoon worm Urechis unicinctus (Drasche, 1880) from three intertidal-flat sites in the Seto Inland Sea represent a new report for the western Japan, and the second for the country. Our morphological observations reveal that the shape of the cephalic peaks in the frontal prostomial margin is variable even within a local population, although this character has been considered as diagnostic for Arctonoella. This genus is closely related with Hesperonoe Chamberlin, 1919, both morphologically and phylogenetically. Hesperonoe urechis Marin and Antokhina, 2020, collected inside a burrow of U. unicinctus in the Russian Far East, is hereby deemed a junior synonym of A. sinagawaensis. This species morphologically resembles Hesperonoe adventor (Skogsberg in Fisher and MacGinitie, 1928), which inhabits spoon worm (Urechis caupo Fisher and MacGinitie, 1928 and Echiurus echiurus alaskanus Fisher, 1946) burrows along the northeastern Pacific coast of America. Therefore, we conclude that the Arctonoella-Hesperonoe species complex requires to be reviewed to determine the proper generic arrangement. Additionally, we revise the available data on the symbiotic fauna living inside the burrows of U. unicinctus and U. caupo.

The aim of this paper is to show that Tilman's graphical method for the study of competition between two species for two resources can be advantageously used for the study of commensalism or syntrophy models, where a first species produces the substrate necessary for the growth of the second species. The growth functions of the species considered are general and include both inhibition by the other substrate and inhibition by the species' limiting substrate, when it is at a high concentration. Because of their importance in microbial ecology, models of commensalism and syntrophy, with or without self-inhibition, have been the subject of numerous studies in the literature. We obtain a unified presentation of a large number of these results from the literature. The mathematical model considered is a differential system in four dimensions. We give a new result of local stability of the positive equilibrium, which has only been obtained in the literature in the case where the removal rates of the species are identical to the dilution rate and the study of stability can be reduced to that of a system in two dimensions. We describe the operating diagram of the system: this is the bifurcation diagram which gives the asymptotic behavior of the system when the operating parameters are varied, i.e., the dilution rate and the substrate inlet concentrations.

Microbial communities play fundamental roles in every complex ecosystem, such as soil, sea and the human body. The stability and diversity of the microbial community depend precisely on the composition of the microbiota. Any change in the composition of these communities affects microbial functions. An important goal of studying the interactions between species is to understand the behavior of microbes and their responses to perturbations. These interactions among species are mediated by the exchange of metabolites within microbial communities. We developed a computational model for the microbial community that has a separate compartment for exchanging metabolites. This model can predict possible metabolites that cause competition, commensalism, and mutual interactions between species within a microbial community. Our constraint-based community metabolic modeling approach provides insights to elucidate the pattern of metabolic interactions for each common metabolite between two microbes. To validate our approach, we used a toy model and a syntrophic co-culture of Desulfovibrio vulgaris and Methanococcus maripaludis, as well as another in co-culture between Geobacter sulfurreducens and Rhodoferax ferrireducens. For a more general evaluation, we applied our algorithm to the honeybee gut microbiome, composed of seven species, and the epiphyte strain Pantoea eucalypti 299R. The epiphyte strain Pe299R has been previously studied and cultured with six different phyllosphere bacteria. Our algorithm successfully predicts metabolites, which imply mutualistic, competitive, or commensal interactions. In contrast to OptCom, MRO, and MICOM algorithms, our COMMA algorithm shows that the potential for competitive interactions between an epiphytic species and Pe299R is not significant. These results are consistent with the experimental measurements of population density and reproductive success of the Pe299R strain. Author summary: Microbial consortia play critical roles in human health and environmental biogeochemical cycles. Studying interactions and communications among organisms is integral for understanding the role of individual microbes in microbial communities. Organisms release and consume metabolites in the extracellular environment, which dictate the assembly and interactions of communities. Researchers have indeed used constraint-based metabolic modeling to analyze the metabolic interactions for multi-organism communities. We propose a computational framework to predict metabolic interactions between pairs of microbial species. We investigate whether, for a specific shared metabolite in the extracellular environment, the two species may have competitive, parasitic, or commensal interactions. These results of our algorithms may help identify important metabolites that shape the interaction patterns in natural communities, and can also be useful for designing media. We demonstrate the applicability of our method by applying it to well-known communities in the honey bee gut microbiota and on leaf surfaces. We then compare the results of our algorithm for the phyllosphere bacterial community with empirical data. [ABSTRACT FROM AUTHOR]

The productivity of agricultural ecosystems is heavily influenced by soil-dwelling organisms. To optimize agricultural practices and management, it is critical to know the composition, abundance, and interactions of soil microorganisms. Our study focused on Acrobeles complexus nematodes collected from tomato fields in South Africa and analyzed their associated bacterial communities utilizing metabarcoding analysis. Our findings revealed that A. complexus forms associations with a wide range of bacterial species. Among the most abundant species identified, we found Dechloromonas sp., a bacterial species commonly found in aquatic sediments, Acidovorax temperans, a bacterial species commonly found in activated sludge, and Lactobacillus ruminis, a commensal motile lactic acid bacterium that inhabits the intestinal tracts of humans and animals. Through principal component analysis (PCA), we found that the abundance of A. complexus in the soil is negatively correlated with clay content (r = -0.990) and soil phosphate levels (r = -0.969) and positively correlated with soil sand content (r = 0.763). This study sheds light on the bacterial species associated to free-living nematodes in tomato crops in South Africa and highlights the occurrence of various potentially damaging and beneficial nematode-associated bacteria, which can in turn, impact soil health and tomato production. [ABSTRACT FROM AUTHOR]

Evaluation of the apportionment of genetic diversity of human bacterial commensals within and between human populations is an important step in the characterization of their evolutionary potential. Recent studies showed a correlation between the genomic diversity of human commensal strains and that of their host, but the strength of this correlation and of the geographic structure among human populations is a matter of debate. Here, we studied the genomic diversity and evolution of the phylogenetically related oro-nasopharyngeal healthy-carriage Streptococcus mitis and Streptococcus pneumoniae, whose lifestyles range from stricter commensalism to high pathogenic potential. A total of 119 S. mitis genomes showed higher within- and among-host variation than 810 S. pneumoniae genomes in European, East Asian and African populations. Summary statistics of the site-frequency spectrum for synonymous and non-synonymous variation and ABC modelling showed this difference to be due to higher ancestral bacterial population effective size (Ne) in S. mitis, whose genomic variation has been maintained close to mutation-drift equilibrium across (at least many) generations, whereas S. pneumoniae has been expanding from a smaller ancestral bacterial population. Strikingly, both species show limited differentiation among human populations. As genetic differentiation is inversely proportional to the product of effective population size and migration rate (Nem), we argue that large Ne have led to similar differentiation patterns, even if m is very low for S. mitis. We conclude that more diversity within than among human populations and limited population differentiation must be common features of the human microbiome due to large Ne. Author summary: The genetic variation of human-associated bacteria and the evolutionary mechanisms leading to that variation are crucial for the establishment of highly contextual interactions with their host, giving rise to phenotypes such as virulence. Here, we studied Streptococcus mitis and Streptococcus pneumoniae, who share a common ancestor but evolved lifestyles on different ends of the pathogenic potential spectrum: S. mitis is mainly commensal, whereas S. pneumoniae has high pathogenic potential. Genomic variation of worldwide healthy-carriage strains is considerably higher for S. mitis. We show this to be due to a larger ancestral population in S. mitis, whose population effective size (Ne) and mutation gain and loss (by genetic drift) have been kept stable over the generations. In contrast, S. pneumoniae population has expanded from an ancestral population with smaller Ne. We also observe low genetic differentiation among populations in both species. We deduce that this is due to large Ne which, even with limited dispersal rate as in S. mitis, leads to significant effective dispersal among populations. As both species' properties of Ne and dispersal are common among human-associated bacteria, more diversity within rather than among human populations and limited population differentiation must be common features of the human microbiome. [ABSTRACT FROM AUTHOR]

Phenotypic heterogeneity poses a significant hurdle for cancer treatment but is under-characterized in the context of tumor invasion. Amidst the range of phenotypic heterogeneity across solid tumor types, collectively invading cells and single cells have been extensively characterized as independent modes of invasion, but their intercellular interactions have rarely been explored. Here, we isolated collectively invading cells and single cells from the heterogeneous 4T1 cell line and observed extensive transcriptional and epigenetic diversity across these subpopulations. By integrating these datasets, we identified laminin-332 as a protein complex exclusively secreted by collectively invading cells. Live-cell imaging revealed that laminin-332 derived from collectively invading cells increased the velocity and directionality of single cells. Despite collectively invading and single cells having similar expression of the integrin a6ß4 dimer, single cells demonstrated higher Rac1 activation upon laminin-332 binding to integrin a6ß4. This mechanism suggests a novel commensal relationship between collectively invading and single cells, wherein collectively invading cells promote the invasive potential of single cells through a laminin-332/Rac1 axis. [ABSTRACT FROM AUTHOR]

Gopher tortoises (Gopherus polyphemus), the only land tortoises native to the southeastern United States, are found throughout their range in a variety of upland habitat types, with their use of upland pine-dominated habitats receiving most attention. Fewer studies have examined their use of coastal beach dune habitats, but some of the highest gopher tortoise burrow densities have been observed in this vulnerable, yet critical, habitat. Gopher tortoises construct extensive burrows for their own use, and these burrows have also been shown to support numerous other animals (i.e., commensal species) that may depend on them for critical needs (e.g., shelter, food). Motion-activated wildlife cameras allow for nonintrusive and continuous observation of burrow activity with minimal disturbance to the animals and habitat. Here we examined 10 gopher tortoise burrows over a 12-mo period using motion-activated wildlife cameras in beach dune habitat in an undeveloped section of coastline in northeast Florida. Gopher tortoises were most frequently observed during the spring and summer months (April–August), and most often during daylight hours. Gopher tortoise behaviors such as burrow maintenance, mating, foraging, and resting were all observed more during April through August, which is a slightly earlier start than these activities have been observed in inland populations. We observed a commensal community of 51 animal taxa using tortoise burrows and their aprons, 29 of which we were able to identify to species. The commensal community was generally similar to those in inland habitats, but we did observe some taxa that were previously undocumented at gopher tortoise burrows including 2 bird species and 8 insect taxa. These commensals displayed varied diel and seasonal activity patterns, with many taxa observed at burrows concurrently occupied by gopher tortoises. Considered together, our observations of gopher tortoise behavior and their commensal community in coastal beach dunes provide valuable insights into the importance of this understudied habitat and highlight distinct differences from inland ecosystems. [ABSTRACT FROM AUTHOR]

Roads have pervasive impacts on wildlife, including habitat loss and fragmentation, road mortality, habitat pollution and increased human use of habitats surrounding them. However, the effects of roads on interspecific interactions are less understood. Here we provide a synthesis of the existing literature on how species interactions may be disrupted by roads, identify knowledge gaps, and suggest avenues for future research and conservation management. We conducted a systematic search using the Web of Science database for each species interaction (predation, competition, mutualism, parasitism, commensalism and amensalism). These searches yielded 2144 articles, of which 195 were relevant to our topic. Most of these studies focused on predation (50%) or competition (24%), and less frequently on mutualism (17%) or, parasitism (9%). We found no studies on commensalism or amensalism. Studies were biased towards mammals from high‐income countries, with most conducted in the USA (34%) or Canada (18%). Our literature review identified several patterns. First, roads disrupt predator–prey relationships, usually with negative impacts on prey populations. Second, new disturbed habitats created in road corridors often benefit more competitive species, such as invasive species, although some native or endangered species can also thrive there. Third, roads degrade mutualistic interactions like seed dispersal and pollination. Fourth, roads can increase parasitism rates, although the intensity of the alteration is species specific. To reduce the negative impacts of roads on interspecific interactions, we suggest the following management actions: (i) verges should be as wide and heterogenous as possible, as this increases microhabitat diversity, thus enhancing ecosystem services like pollination and seed dispersal; (ii) combining different mowing regimes can increase the complexity of the habitat corridor, enabling it to act as a habitat for more species; (iii) the use of de‐icing salts should be gradually reduced and replaced with less harmful products or maintenance practices; (iv) wildlife passes should be implemented in groups to reduce animal concentrations inside them; (v) periodic removal of carcasses from the road to reduce the use of this resource by wildlife; and (vi) implementation of traffic‐calming schemes could enhance interspecific interactions like pollination and avoid disruption of predator–prey relationships. [ABSTRACT FROM AUTHOR]

This paper contributes to the research on the symbiotic relationship between religion and the market by examining the nature and implications of the marketization of religion in a contemporary Christendom in which religion and the market are hegemonic. Based on our analysis of 3741 church advertisements in Ghana over a 6-year period, we conceptualize three symbiotic relationships that coexist between the market and religion—commensalism, mutualism, and competition. We argue that these symbiotic relationships mirror how religion hegemonizes popular imagination and members' consumption through marketization in contemporary Christendom. This study extends our understanding of the dialectical relationship between religion and the market by showing that religion can use marketization to perpetuate its hegemony within and beyond the market. [ABSTRACT FROM AUTHOR]

For perennial plants, newly emerged organs are fresh hot spots for environmental microbes to occupy and assemble to form mature microbial communities. In the microbial community, some commensal fungi can play important roles in microbial succession, thus significantly improving host plant growth and disease resistance. However, their participating patterns in microbial assembly and succession remain largely unknown. In this study, we profiled the fungal community and found a similar fungal succession pattern of spring-emerged leaves from March to October in two pomelo orchards. Specifically, the fungal species, tracked on the old leaves, dominated the spring leaves after emergence and then decreased in relative abundance. This reduction in priority effects on the spring leaves was then followed by an increase in the number of observed species, Shannon and phylogenetic diversity indices, and the pathogen-associated fungal groups. In addition, we found that the temporal fungal succession on the spring leaves highly correlated with the disease occurrence in the orchards and with the temperature and precipitation variation from spring to summer. Of the pathogen-associated fungal groups, an increase in the relative abundance of Mycosphaerellaceae, hosting the causal agent of citrus greasy spot, correlated with the occurrence of the disease, while the relative abundance of Diaporthaceae, hosting the causal agent of melanose, was extremely low during the fungal succession. These results confirm that the two kinds of pathogen-associated fungal groups share different lifestyles on citrus, and also suggest that the study of temporal fungal succession in microbial communities can add to our understanding of the epidemiology of potential plant pathogens. [ABSTRACT FROM AUTHOR]

Background: Metritis is a prevalent uterine disease that affects the welfare, fertility, and survival of dairy cows. The uterine microbiome from cows that develop metritis and those that remain healthy do not differ from calving until 2 days postpartum, after which there is a dysbiosis of the uterine microbiome characterized by a shift towards opportunistic pathogens such as Fusobacteriota and Bacteroidota. Whether these opportunistic pathogens proliferate and overtake the uterine commensals could be determined by the type of substrates present in the uterus. The objective of this study was to integrate uterine microbiome and metabolome data to advance the understanding of the uterine environment in dairy cows that develop metritis. Holstein cows (n = 104) had uterine fluid collected at calving and at the day of metritis diagnosis. Cows with metritis (n = 52) were paired with cows without metritis (n = 52) based on days after calving. First, the uterine microbiome and metabolome were evaluated individually, and then integrated using network analyses. Results: The uterine microbiome did not differ at calving but differed on the day of metritis diagnosis between cows with and without metritis. The uterine metabolome differed both at calving and on the day of metritis diagnosis between cows that did and did not develop metritis. Omics integration was performed between 6 significant bacteria genera and 153 significant metabolites on the day of metritis diagnosis. Integration was not performed at calving because there were no significant differences in the uterine microbiome. A total of 3 bacteria genera (i.e. Fusobacterium, Porphyromonas, and Bacteroides) were strongly correlated with 49 metabolites on the day of metritis diagnosis. Seven of the significant metabolites at calving were among the 49 metabolites strongly correlated with opportunistic pathogenic bacteria on the day of metritis diagnosis. The main metabolites have been associated with attenuation of biofilm formation by commensal bacteria, opportunistic pathogenic bacteria overgrowth, tissue damage and inflammation, immune evasion, and immune dysregulation. Conclusions: The data integration presented herein helps advance the understanding of the uterine environment in dairy cows with metritis. The identified metabolites may provide a competitive advantage to the main uterine pathogens Fusobacterium, Porphyromonas and Bacteroides, and may be promising targets for future interventions aiming to reduce opportunistic pathogenic bacteria growth in the uterus. [ABSTRACT FROM AUTHOR]

The transition between yeast and hyphae is crucial for regulating the commensalism and pathogenicity in Candida albicans. The mechanisms that affect the invasion of hyphae in solid media, whose deficiency is more related to the pathogenicity of C. albicans, have not been elucidated. Here, we found that the disruption of VAM6 or VPS41 which are components of the homotypic vacuolar fusion and protein sorting (HOPS) complex, or the Rab GTPase YPT72, all responsible for vacuole fusion, led to defects in hyphal growth in both liquid and solid media, but more pronounced on solid agar. The phenotypes of vac8Δ/Δ and GTR1OE-vam6Δ/Δ mutants indicated that these deficiencies are mainly caused by the reduced mechanical forces that drive agar and organs penetration, and confirmed that large vacuoles are required for hyphal mechanical penetration. In summary, our study revealed that large vacuoles generated by vacuolar fusion support hyphal penetration and provided a perspective to refocus attention on the role of solid agar in evaluating C. albicans invasion. The transition between yeast and hyphae is crucial for the pathogenicity of Candida albicans. Here, Liu et al. show that vacuole fusion is active during hyphal extension and that large vacuoles increase the mechanical forces of hyphae penetrating into organs. [ABSTRACT FROM AUTHOR]

An accurate understanding of the ecology and complexity of the poultry respiratory microbiota is of utmost importance for elucidating the roles of commensal or pathogenic microorganisms in the respiratory tract, as well as their associations with health or disease outcomes in poultry. This comprehensive review delves into the intricate aspects of the poultry respiratory microbiota, focusing on its colonization patterns, composition, and impact on poultry health. Firstly, an updated overview of the current knowledge concerning the composition of the microbiota in the respiratory tract of poultry is provided, as well as the factors that influence the dynamics of community structure and diversity. Additionally, the significant role that the poultry respiratory microbiota plays in economically relevant respiratory pathobiologies that affect poultry is explored. In addition, the challenges encountered when studying the poultry respiratory microbiota are addressed, including the dynamic nature of microbial communities, site-specific variations, the need for standardized protocols, the appropriate sequencing technologies, and the limitations associated with sampling methodology. Furthermore, emerging evidence that suggests bidirectional communication between the gut and respiratory microbiota in poultry is described, where disturbances in one microbiota can impact the other. Understanding this intricate cross talk holds the potential to provide valuable insights for enhancing poultry health and disease control. It becomes evident that gaining a comprehensive understanding of the multifaceted roles of the poultry respiratory microbiota, as presented in this review, is crucial for optimizing poultry health management and improving overall outcomes in poultry production. [ABSTRACT FROM AUTHOR]

A role for vitamin D in immune modulation and in cancer has been suggested. In this work, we report that mice with increased availability of vitamin D display greater immune-dependent resistance to transplantable cancers and augmented responses to checkpoint blockade immunotherapies. Similarly, in humans, vitamin D-induced genes correlate with improved responses to immune checkpoint inhibitor treatment as well as with immunity to cancer and increased overall survival. In mice, resistance is attributable to the activity of vitamin D on intestinal epithelial cells, which alters microbiome composition in favor of Bacteroides fragilis, which positively regulates cancer immunity. Our findings indicate a previously unappreciated connection between vitamin D, microbial commensal communities, and immune responses to cancer. Collectively, they highlight vitamin D levels as a potential determinant of cancer immunity and immunotherapy success. [ABSTRACT FROM AUTHOR]

The Galeommatoidea are a diverse but little-studied group of small bivalves, well known for the symbiotic relationships many species have with a range of invertebrate taxa. Four species collected from the Western Cape region of South Africa were examined and illustrated, providing new details on their habitat preferences, and depicting the mantle structure of live specimens for the first time. Brachiomya ducentiunus sp. nov., is described herein, and an additional record of Montacuta substriata (Montagu, 1808) is reported from South Africa. Brachiomya ducentiunus and Montacuta substriata have obligate symbiotic relationships with different burrowing echinoids, while Kellia becki (WH Turton, 1932) and Melliteryx mactroides (Hanley, 1857) are free-living. DNA data and phylogenetic analyses are provided for three of the species. [ABSTRACT FROM AUTHOR]

Interactions within the tick microbiome involving symbionts, commensals, and tick‐borne pathogens (TBPs) play a pivotal role in disease ecology. This study explored temporal changes in the microbiome of Rhipicephalus microplus, an important cattle tick vector, focusing on its interaction with Anaplasma marginale. To overcome limitations inherent in sampling methods relying on questing ticks, which may not consistently reflect pathogen presence due to variations in exposure to infected hosts in nature, our study focused on ticks fed on chronically infected cattle. This approach ensures continuous pathogen exposure, providing a more comprehensive understanding of the nesting patterns of A. marginale in the R. microplus microbiome. Using next‐generation sequencing, microbiome dynamics were characterized over 2 years, revealing significant shifts in diversity, composition, and abundance. Anaplasma marginale exhibited varying associations, with its increased abundance correlating with reduced microbial diversity. Co‐occurrence networks demonstrated Anaplasma's evolving role, transitioning from diverse connections to keystone taxa status. An integrative approach involving in silico node removal unveils the impact of Anaplasma on network stability, highlighting its role in conferring robustness to the microbial community. This study provides insights into the intricate interplay between the tick microbiome and A. marginale, shedding light on potential avenues for controlling bovine anaplasmosis through microbiome manipulation. [ABSTRACT FROM AUTHOR]

This article discusses the need for a better understanding of local adaptation in natural populations of ectomycorrhizal (ECM) fungi, which play a crucial role in mutualistic interactions in forest ecosystems. The article highlights a symposium that brought together experts in ecological genomics to discuss the latest advances and prospects in the study of population and landscape genomics of ECM fungi. The symposium covered topics such as tracking patterns of local adaptation, the role of environmental factors, and the use of genotyping technologies. The article also mentions emerging model organisms for studying the genomics of environmental adaptation in ECM fungi. The authors emphasize the importance of interdisciplinary collaborations to advance the field and improve our understanding of these important organisms. [Extracted from the article]

Introduction: Endosymbiotic Wolbachia bacteria are widespread in nature, present in half of all insect species. The success of Wolbachia is supported by a commensal lifestyle. Unlike bacterial pathogens that overreplicate and harm host cells, Wolbachia infections have a relatively innocuous intracellular lifestyle. This raises important questions about how Wolbachia infection is regulated. Little is known about how Wolbachia abundance is controlled at an organismal scale. Methods: This study demonstrates methodology for rigorous identification of cellular processes that affect whole-body Wolbachia abundance, as indicated by absolute counts of the Wolbachia surface protein (wsp) gene. Results: Candidate pathways, associated with well-described infection scenarios, were identified. Wolbachia-infected fruit flies were exposed to small molecule inhibitors known for targeting those same pathways. Sequential tests in D. melanogaster and D. simulans yielded a subset of chemical inhibitors that significantly affected whole-body Wolbachia abundance, including the Wnt pathway disruptor, IWR-1 and the mTOR pathway inhibitor, Rapamycin. The implicated pathways were genetically retested for effects in D. melanogaster, using inducible RNAi expression driven by constitutive as well as chemically-induced somatic GAL4 expression. Genetic disruptions of armadillo, tor, and ATG6 significantly affected whole-body Wolbachia abundance. Discussion: As such, the data corroborate reagent targeting and pathway relevance to whole-body Wolbachia infection. The results also implicate Wnt and mTOR regulation of autophagy as important for regulation of Wolbachia titer. [ABSTRACT FROM AUTHOR]

Natural processes and patterns are altered by human activity at different spatial and temporal scales, affecting species assemblages and population traits, modifying mechanisms or regulating dynamics at different scales. However, little is known about the influence of landscape structure on small mammal assemblages and populations on farms. Thus, in this work, we aimed to study the effect of landscape and environmental characteristics at the farm scale on the assemblage and populations of native and introduced small mammals in pig and dairy farms located in Buenos Aires province, Argentina. Our results showed that farms in contexts of higher environmental diversity at the landscape scale have higher species richness. Our results also showed that variations in assemblage composition were associated with the quantity of water body surfaces, cattle food, small mammal refugia, and impervious surfaces at the farm scale—and with woodland, grassland, and natural vegetation cover at the landscape scale. The abundance of commensal murids was higher on farms near towns, with higher vegetation cover at the farm scale and/or in landscape contexts with fewer crops. The abundance of Akodon azarae was higher on farms with a lower amount of cattle food at the farm scale and crop patches in the landscape. The abundance of Didelphis albiventris was higher during spring on farms with a low proportion of bare ground, while that of Lutreolina crassicaudata was higher on farms with high vegetation cover and a lower number of water body surfaces. These results show the relevance of multiscale determinants in the development of ecologically based management strategies to control pest small mammals. [ABSTRACT FROM AUTHOR]

Positive interactions are underrepresented in marine ecology but have a substantial impact on biodiversity and ecosystem stability. Here, we showcase a previously undescribed commensal relationship between two temperate rocky reef fishes in sandy bottom habitats: the rock wrasse (Halichoeres semicinctus) and round stingray (Urobatis halleri). Using snorkel surveys in Big Fisherman's Cove on Santa Catalina Island, we showed that rock wrasse abundances were positively associated with the presence of round stingrays and that round stingrays significantly altered rock wrasse behavior. Specifically, rock wrasse within a 1 m radius of a feeding round stingray spent approximately 40% and 35% more time feeding compared to rock wrasse in proximity of a resting round stingray or a sandy bottom control, respectively. The positive effect of feeding round stingrays on rock wrasse feeding behavior is in response to stingrays disturbing sand as they eat, uncovering small invertebrates for the wrasses to prey on. As round stingrays are one of the most common fishes in southern California, they may impact the fitness of rock wrasses. [ABSTRACT FROM AUTHOR]

Dead coral rocks are prevalent hard substrates in shallow warm waters, providing habitat for various infaunal and boring invertebrates. Despite this, the nature of species interactions, especially symbiotic relationships, among them remains poorly understood. Bonellia (Annelida: Thalassematidae: Bonelliinae) is a group of greenish echiuran worms commonly inhabiting cavities inside dead coral rocks. Although echiuran burrows in marine sediments are known to harbour various host-specific macrosymbionts, it remains unclear whether such associations also occur in hard substrates. To address this, we investigated the diversity of macrosymbionts associated with the burrows of Bonellia sp. aff. minor in the warm-temperate coast of the Kii Peninsula, Japan, and the evolutionary origins of those symbionts. The host's burrow morphology was also examined using micro-computed tomography (CT) scanning. Our field survey revealed that the burrows of Bo. sp. aff. minor hosted three commensal species including a polychaete, Oxydromus fauveli , and two new species, a bivalve (Basterotia bonelliphila sp. nov.) and an amphipod (Leucothoe bonelliae sp. nov.). Our molecular phylogenetic analyses showed that each symbiont species belongs to a clade comprising commensal species specific to echiurans or annelids. Overall, our findings contribute to a better understanding of symbiotic associations in marine hard substrates. [ABSTRACT FROM AUTHOR]

Symbionts dominate planetary diversity and three primary symbiont diversification processes have been proposed: co-speciation with hosts, speciation by host-switching, and within-host speciation. The last mechanism is prevalent among members of an extraordinary marine symbiosis in the Indian River Lagoon, Florida, composed of a host mantis shrimp, Lysiosquilla scabricauda, and seven host-specific commensal vasconielline “yoyo” clams (Galeommatoidea) that collectively occupy two distinct niches: burrow-wall-attached, and host-attached/ectocommensal. This within-host symbiont radiation provides a natural experiment to test how symbiont coexistence patterns are regulated in a common ancestral habitat. The competitive exclusion principle predicts that sister taxa produced by adaptive speciation (with distinct morphologies and within-burrow niches) are most likely to coexist whereas the neutral theory predicts no difference among adaptive and non-adaptive sister taxa co-occurrence. To test these predictions, we engaged in (1) field-censusing commensal species assemblages; (2) trophic niche analyses; (3) laboratory behavioral observations. Although predicted by both models, the field census found no mixed-niche commensal assemblages: multi-species burrows were exclusively composed of burrow-wall commensals. Their co-occurrence matched random assembly process expectations, but presence of the single ectocommensal species had a highly significant negative effect on recruitment of all burrow-wall commensal species (P

Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities. Predicting the colonization of exogenous species in complex communities is a challenge in ecology. Here, the authors propose a data-driven approach to predict colonization outcomes and perform validation experiments in human gut microbial communities. [ABSTRACT FROM AUTHOR]

In this review, we address the interplay between the complement system and host microbiomes in health and disease, focussing on oral bacteria known to contribute to homeostasis or to promote dysbiosis associated with dental caries and periodontal diseases. Host proteins modulating complement activities in the oral environment and expression profiles of complement proteins in oral tissues were described. In addition, we highlight a sub-set of bacterial proteins involved in complement evasion and/or dysregulation previously characterized in pathogenic species (or strains), but further conserved among prototypical commensal species of the oral microbiome. Potential roles of these proteins in host-microbiome homeostasis and in the emergence of commensal strain lineages with increased virulence were also addressed. Finally, we provide examples of how commensal bacteria might exploit the complement system in competitive or cooperative interactions within the complex microbial communities of oral biofilms. These issues highlight the need for studies investigating the effects of the complement system on bacterial behaviour and competitiveness during their complex interactions within oral and extra-oral host sites. [ABSTRACT FROM AUTHOR]

Dr. Bénédicte Boisseron's book, "Afro-Dog: Blackness and the Animal Question," provides a nuanced analysis of the relationship between racism and speciesism. Boisseron explores the historical and cultural dimensions of the association between Black people and dogs, highlighting the gendered and subaltern dimensions of this discourse. She also introduces the concept of "commensal dogs," which challenges the assumption of power differentials in cross-species encounters and offers a path for a different politics of relationship. Boisseron's book contributes to the discussion of racism and speciesism by emphasizing the need for an anti-anthropocentric approach to power, domination, and oppression. [Extracted from the article]

This review explores the 'gut–lung axis' in asthma with a focus on commensal fungal organisms. We explore how changes to the intestinal commensal fungal community composition alter lung immune function. We comprehensively review available studies that have profiled the composition of the gut mycobiome in adults and children with asthma, and discuss mechanisms of gut–lung interactions that have been described in animal models of asthma. Studies indicate that intestinal fungal dysbiosis, such as an increased abundance of certain fungi like Candida, can elevate the risk of asthma in children and exacerbate it in adults. This effect is mediated through various pathways: the host immune system's sensing of dysbiosis via C-type lectin receptors (e.g., Dectin-2), the impact of pro-inflammatory fungal metabolites (e.g., 12,13-diHOME, prostaglandin E2), and the role of lung immune cells (e.g., group 2 innate lymphoid cells [ILC2], M2 macrophages). We also describe strategies for modulating the gut mycobiome as potential therapies for severe asthma. The review concludes by emphasizing the necessity for further research into the role of the gut mycobiome in asthma to deepen our understanding of these complex interactions. [ABSTRACT FROM AUTHOR]

The brown-banded cockroach (Supella longipalpa) is a widespread nuisance and public health pest. Like the German cockroach (Blattella germanica), this species is adapted to the indoor biome and completes the entirety of its life cycle in human-built structures. Recently, understanding the contributions of commensal and symbiotic microbes to the biology of cockroach pests, as well as the applications of targeting these microbes for pest control, have garnered significant scientific interest. However, relative to B. germanica, the biology of S. longipalpa, including its microbial associations, is understudied. Therefore, the goal of the present study was to quantitatively examine and characterize both the endosymbiont and gut bacterial communities of S. longipalpa for the first time. To do so, bacterial 16S rRNA gene amplicon sequencing was conducted on DNA extracts from whole adult females and males, early instar nymphs, and late instar nymphs. The results demonstrate that the gut microbiome is dominated by two genera of bacteria known to have beneficial probiotic effects in other organisms, namely Lactobacillus and Akkermansia. Furthermore, our data show a significant effect of nymphal development on diversity and variation in the gut microbiome. Lastly, we reveal significant negative correlations between the two intracellular endosymbionts, Blattabacterium and Wolbachia, as well as between Blattabacterium and the gut microbiome, suggesting that Blattabacterium endosymbionts could directly or indirectly influence the composition of other bacterial populations. These findings have implications for understanding the adaptation of S. longipalpa to the indoor biome, its divergence from other indoor cockroach pest species such as B. germanica, the development of novel control approaches that target the microbiome, and fundamental insect-microbe interactions more broadly. [ABSTRACT FROM AUTHOR]

Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis. [ABSTRACT FROM AUTHOR]

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Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant–microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop–microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant–microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness. [ABSTRACT FROM AUTHOR]

Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome. [ABSTRACT FROM AUTHOR]